The range of values for the AP

[shenlinyong]

My understanding is that the same size of the TAD, the larger the AP value, the stronger and more concentrated the interaction within the TAD. But I don't know why the AP values in my result file have 0 and -1. Does 0 mean that there is no interaction within the TAD? What does -1 mean?

1 ChromID Start   End     AP      Gap-Ratio
      2 chr1    0       150000  -1      1.0
      3 chr1    150000  360000  -1      1.0
      4 chr1    360000  440000  -1      1.0
      5 chr1    440000  860000  0.8188976152072527      0.16666666666666663
      6 chr1    860000  1200000 -1      0.5882352941176471
      7 chr1    1200000 1750000 0.7044267450521011      0.054545454545454564
      8 chr1    1750000 3570000 0.16778573192589943     0.11538461538461542
      9 chr1    3570000 4190000 0.6700936296963629      0.0
     10 chr1    4190000 4330000 0       0.0
     11 chr1    4330000 4690000 -1      0.25
     12 chr1    4690000 5640000 0.3859107300537907      0.08421052631578951
     13 chr1    5640000 6650000 0.31304512317832633     0.0

[XiaoTaoWang]

0 means there are fewer than 3 significant interactions within a TAD, and -1 simply indicates there are too many vacant columns/rows within a TAD.

[shenlinyong]

Your answer is so perfect, thank you so much.